Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30057 discussions

mri_fuse_segmentation error: could not open file
by Tommaso Cusolito S319624 04 Jun '24

04 Jun '24

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to extract cortical thickness from a fifth scan using a template based on only the first four scans (obtained by following the longitudinal pipeline available at https://secure-web.cisco.com/1S7BQNmF9HghVT1XkcD-pYvMmoQDm0WTjg3-N1bP-4anPW…) Unfortunately, I don't have the option to run the longitudinal processing from scratch including the fifth scan as I no longer have access to the cross-sectionally processed single scan data (in format patient_scan#) for scans 1 through 4 but only to the folders generated by the recon-all function (in format patient_scan#.long.patient_template). I've made sure to generate .lta files (through mri_robust_register) for forwards and backwards transformations from s5 to template and to add the scan 5 to the "base-tps" file, but recon-all reports a later error when using the function mri_fuse_segmentations as I no longer have access to files for single scans (norm.mgz, aseg.mgz,aseg.auto_noCCseg.mgz). I acknowledge that the template data will be biased towards the first four scans but I was looking for a way to use the function on only data belonging to the "patient_scan#.long.patient_template" folders together with the fifth scan data "patient_s5". Has anyone tried using this course of action and found a viable solution? I've attached the recon-all.log in case it's of any use. 1) FreeSurfer version: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 2) Platform: 3.10.0-1160.92.1.el7.x86_64 3) uname -a: Linux krusty 3.10.0-1160.92.1.el7.x86_64 #1 SMP Tue Jun 20 11:48:01 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux 4) recon-all.log: see attached

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fmriprep and freesurfer license
by Patterson, Dianne K - (dkp) 03 Jun '24

03 Jun '24

External Email - Use Caution I use this on our HPC: apptainer run --cleanenv --bind ${MRIS}/data:/data:ro --bind ${MRIS}/derivatives/fmriprep:/outputs --bind ${MRIS}/fmriprep_work:/work ${APP} /data /outputs participant --participant_label ${Subject} --fs-license-file ${HOME}/license.txt -w /work --stop-on-first-crash --ignore slicetiming --cifti-output --output-spaces fsnative fsaverage MNI152NLin6Asym:res-2 This assumes license.txt is in my home directory. -Dianne Dianne Patterson, Ph.D<https://profiles.arizona.edu/person/dkp> dkp(a)arizona.edu Office: BSRL, Room 235 RII Neuroimaging Staff Scientist Program Coordinator Neuroimaging Methods Certificate<https://cogsci.arizona.edu/programs/certificate> Cognitive Science GIDP affiliate member Faculty Lead OpenClass.ai<https://openclass.ai> Mastodon: @dpat@scicomm.xyz

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Re: [Freesurfer] Contrast files - 2 groups, 4 covariates
by Liliana Wu 03 Jun '24

03 Jun '24

External Email - Use Caution Thank you Douglas. That’s much clearer. I do however, have a subject without a gender disclosure. Would I set up my class and contrasts as: 5 classes: PatentientsMale, PatientsFemale, HCMale, HCFemale, HCNa then use contrast [0.5 0.5 -0.33 -0.33 -0.33 0 0 0 0 0 ...]? Best, Liliana

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Call for applications: LINC fellows program 2024-25
by Yendiki, Anastasia 31 May '24

31 May '24

Dear FreeSurfers - Our BRAIN Initiative funded center for Large-scale Imaging of Neural Circuits (LINC)<https://connects.mgh.harvard.edu/> is seeking to name 2 undergrads and 2 postdocs from diverse backgrounds and/or under-resourced institutions “LINC fellows” for 2024-25. The applicants are expected to have a research mentor in their home institution, who will provide a letter of support for their application. During the LINC fellowship year, the LINC fellows will remain in their current program/institution, and engage in a research project that can benefit from remote access to the data and computational resources of the LINC project, and collaboration with the LINC investigative team. For eligibility and application materials, please see: https://connects.mgh.harvard.edu/outreach/<https://connects.mgh.harvard.edu/outreach/#research-teams> Thank you for sharing with any qualified applicants that you may know! Anastasia. | Anastasia Yendiki, Ph.D. | Associate Professor, Harvard Medical School | Associate Investigator, Massachusetts General Hospital | 149 13th St. Suite 2301 | Charlestown, MA 02129 | Tel: 617-726-9434 | Fax: 617-726-7422 | Web: http://dmri.mgh.harvard.edu/a-y

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Re: [Freesurfer] License for FreeSurfer 5.x
by fsbuild 30 May '24

30 May '24

External Email - Use Caution  Hello Rafa, If you take a look under, https://secure-web.cisco.com/1dfxSJC8JWSEz6n8dSa8oPi0pnwDlx9137h03BernH-2Q8… - you will see there is a Virtual Box ..vdi file for the 5.3.0 release,  https://secure-web.cisco.com/1RcGOCq2p6BYFO6rvNlcGnNuDdMKQaAC7luBVOPnx9yiqM… - but I think that Virtual Box image will be running CentOS6 (or some old version of CentOS).  At that time we did not build or provide releases for Ubuntu linux.  The version of CentOS in the VM and Ubuntu12 may use different versions of glibc so I’m not sure the packages with 5.3.0 binaries listed above will run on Ubuntu12. We advertise the following caveat about switching to newer/different OS versions, or upgrading to a different (newer) Freesurfer release built with different compilers.  Either of those changes will likely produce some difference in floating point math results. Important Note: When processing a group of subjects for your study, it is essential to process all your subjects with the same version of FreeSurfer, on the same OS platform and vendor, and for safety, even the same version of the OS. While we continue to work to ensure that results match across platforms, there are none-the-less system-level libraries that are OS dependent. An exception to this rule is that you may view and edit files across any platform or version, and run some post-processing tools (outside the recon-all stream) if you check with us first (for instance you may run the longitudinal processing with newer versions). But if it’s not an issue for you to run on an old version of CentOS instead of Ubuntu linux, then your best bet is to try and run the existing .vdi file listed above in the VirtualBox client - which you would need to download and install on your current Linux machine. -R. On May 30, 2024, at 12:34, Rafael Navarro <rafa.navarrogo(a)gmail.com> wrote:        External Email - Use Caution        Hello everyone,  I am working with a neuroimage model that uses the FreeSurfer 5.3 version as preprocessing (only autorecon-I). I have tried to install Freesurfer 5.3, but after reading previous messages in the mailing list It seems the license file format changed from FreeSurfer 5.3 to 6.0 due to an update of the Ubuntu libcrypt. Do you think that migrating the autorecon-I from v5.3 to v6.0 might affect the final results? Is there any alternative? Does a docker container running Ubuntu 12 with FreeSurfer 5.3 could work? Is still possible to get a license with the old format?  Regards! Rafa Navarro  _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1rQmyzrBzuTiOfJNym0JFZOqwWej3pdzcvkhiXJWLyPV3L…

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License for FreeSurfer 5.x
by Rafael Navarro 30 May '24

30 May '24

External Email - Use Caution Hello everyone, I am working with a neuroimage model that uses the FreeSurfer 5.3 version as preprocessing (only autorecon-I). I have tried to install Freesurfer 5.3, but after reading previous messages in the mailing list It seems the license file format changed from FreeSurfer 5.3 to 6.0 due to an update of the Ubuntu libcrypt. Do you think that migrating the autorecon-I from v5.3 to v6.0 might affect the final results? Is there any alternative? Does a docker container running Ubuntu 12 with FreeSurfer 5.3 could work? Is still possible to get a license with the old format? Regards! Rafa Navarro

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Re: [Freesurfer] SynthSR problem
by fsbuild 28 May '24

28 May '24

External Email - Use Caution  Some commands such as mri_synthsr in previous releases, e.g., 7.4.1, use code built with Intel processor specific instructions that cannot run on an arm processor, i.e., there is not full backwards binary compatibility in that case using the Rosetta emulation environment on MacOS.  Hence the “illegal instruction” error. We do have a (more recent) development build on a Silicon Mac you can download via the link,  https://secure-web.cisco.com/1lWnZREm3JXXMeuMNsb_hOkyb2ipaBFlFN8u43RUzyQ6-c… .... it has not yet gone the the same testing as done for a release.  Please let us know if you run into issues trying it. - R. On May 28, 2024, at 16:08, Tabasi, Farhad <farhad-tabasi(a)uiowa.edu> wrote:        External Email - Use Caution        Hello FreeSurfer developers, I am trying to use mri_synthsr to improve the quality of clinical scans, but this is the error I encountered: Illegal instruction: 4 (I followed the instructions on SynthSR page, using mri_synthsr --i input.nii --o output_synthT1.nii command) FreeSurfer version: freesurfer-darwin-macOS-7.3.2-20220804-6354275OS: macOS Ventura (13.2.1) on iMac M1 (116 GB) This is likely related to binary problems or CPU compatibility (especially with M1).Is there any solution to the issue? Thanks,Farhad Farhad Tabasi, MD (he/him/his)Postdoctoral ScholarHuman Brain Research Lab, Department of Neurosurgery, Carver College of Medicine, University of IowaCell: (858)588-2779_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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SynthSR problem
by Tabasi, Farhad 28 May '24

28 May '24

External Email - Use Caution Hello FreeSurfer developers, I am trying to use mri_synthsr to improve the quality of clinical scans, but this is the error I encountered: Illegal instruction: 4 (I followed the instructions on SynthSR page, using mri_synthsr --i input.nii --o output_synthT1.nii command) FreeSurfer version: freesurfer-darwin-macOS-7.3.2-20220804-6354275 OS: macOS Ventura (13.2.1) on iMac M1 (116 GB) This is likely related to binary problems or CPU compatibility (especially with M1). Is there any solution to the issue? Thanks, Farhad Farhad Tabasi, MD (he/him/his) Postdoctoral Scholar Human Brain Research Lab, Department of Neurosurgery, Carver College of Medicine, University of Iowa Cell: (858)588-2779

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Errors with Recon-all
by yuanyuelunar 28 May '24

28 May '24

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Re: [Freesurfer] Group Stats for hipposubfields, brainstem and amygdalar
by fsbuild 27 May '24

27 May '24

External Email - Use Caution  If you still have the VM setup on your machine, you can open a new terminal window and then you should see the Freesurfer Environment is setup, FREESURFER_HOME   /home/developer/7.2.0/dev FSFAST_HOME       /home/developer/7.2.0/dev/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR      /home/developerfreesurfer/7.2.0/subjects MNI_DIR           /home/developer/7.2.0/mni garnet2[0]:tmp$ ls $FREESURFER_HOME/bin/aparc* The aparc* and aseg* commands should all be in your path, i.e. $ which aparc_stats_aseg /home/developer/7.2.0/bin/aparc_stats_aseg $ which aparcstats2table /home/developer/7.2.0/bin/aparcstats2table $ which aparcstatsdiff /home/developer/7.2.0/bin/aparcstatsdiff $ which aparc2feat /home/developer/7.2.0/bin/aparc2feat $ which aseg2feat /home/developer/7.2.0//bin/aseg2feat $ which asegstats2table /home/developer/7.2.0//bin/asegstats2table $ which asegstatsdiff /home/developer/7.2.0//bin/asegstatsdiff You should be able to get some info about the commands using the "-h" or help option. garnet2[0]:tmp$ aparcstats2table -h Usage: Converts a cortical stats file created by recon-all and or mris_anatomical_stats (eg, ?h.aparc.stats) into a table in which each line is a subject and each column is a parcellation. By default, the values are the area of the parcellation in mm2. The ... ..... rest of output deleted .... - R. On 5/21/24 07:45, Carina Obermüller (carina.obermueller(a)live.at) wrote: External Email - Use Caution Dear Freesurfer team, I am looking for a group stats command like the asegstats2table and aparcstats2table command for hipposubfields, brainstem and amygdalar, but I couldn’t find it in the archives. I remember it was mentioned in the recent Freesurfer course, but I can’t find it anymore. Could you help me out? Also more generally, is there an overview page of all the possible group stats commands? Thank you so much in advance for your reply! Sincerely, Carina _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1zf0G1ETkn7CuwsYRmLLhHlYlAkhG2RaT4vLqBGQDlX4Ki… The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/1nGDgYhKOmxBKFFUQGUJR-tfzcA07RiW6HdqaGmQhhm7ox… <https://secure-web.cisco.com/1Crcaw7mICueLIIsrf-d6bd1LvI1_sMpz1sWUC1sUwcOBxZk8BgT8pV0i4V2CZCwMTxr_9fRoaHE3cOckOu2pVESVMPnvAQ8KkAgNg4T-RBDDg6VcWw0ZViIUP3UwrjMUc8QNtANpWoLDf6gbK2fj3YudolW0E8dn1jomEY9lZ84NUS8TRtbDpyEgxh3lNzZ3maodr_8WIVWzEou_35bn_LyQzHsktG4nkBada5DMmk-1MyVlshU9dVAnjsHRtVs5ma3s3hiKNw9-22D5Y6RdGm034qaJVD1S0JbIIhTa4hiJqltZvP0m9Mar7Nrn3Opj/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline%26gt; . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

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